BN1361 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 1.5669e-06 1.5810e-04
Layer 3 9.0489e-06 1.5233e-03
Layer 5 3.0666e-05 2.4111e-04
Layer 2 5.0774e-05 2.6536e-02
Layer 6 1.3784e-04 6.0406e-04
WM 7.8301e-02 3.2905e-01
Layer 1 9.2329e-01 6.9493e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 6 2.8027 0.7735
RGS4 Layer 5 2.5723 0.7398
TAGLN3 Layer 5 2.3867 0.7398
CPLX1 Layer 5 2.8281 0.7336
CABP1 Layer 6 2.4883 0.7313
SYNGR1 Layer 5 2.3496 0.7223
SYP Layer 6 2.4238 0.7220
ATP6V1F Layer 5 2.2422 0.7157
YPEL3 Layer 4 2.4785 0.7157
GHITM Layer 4 2.4336 0.7157
FLOT1 Layer 4 2.3965 0.7145
GUCY1B1 Layer 5 2.3594 0.7125
COX7A1 Layer 6 2.3965 0.7124
RAB3A Layer 5 2.3027 0.7114
TOLLIP Layer 5 2.4512 0.7109
EPS15 Layer 5 2.5391 0.7107
RUNDC3A Layer 5 2.3105 0.7100
RNF11 Layer 4 2.4863 0.7098
CNTN1 Layer 6 2.4668 0.7097
CHGA Layer 4 2.6016 0.7093
KIF1A Layer 5 2.2266 0.7045
HK1 Layer 5 2.4238 0.7031
STX1B Layer 5 2.4814 0.7029
APBB1 Layer 5 2.2578 0.7020
NDUFB8 Layer 5 2.1816 0.7010
ATP13A2 Layer 5 2.5303 0.6997
CEND1 Layer 6 2.5898 0.6987
AMPH Layer 4 2.5586 0.6980
ATP6V0B Layer 6 2.3184 0.6979
REEP5 Layer 4 2.2871 0.6972
SEZ6L2 Layer 5 2.4883 0.6965
ATP5F1A Layer 4 2.3867 0.6963
GOT1 Layer 4 2.3652 0.6959
SERINC3 Layer 6 2.1621 0.6957
BSN Layer 5 2.4941 0.6950
PFKP Layer 5 2.8184 0.6933
MOAP1 Layer 5 2.6309 0.6928
MGST3 Layer 5 2.4336 0.6925
AGAP3 Layer 5 2.4336 0.6921
SH3GL2 Layer 6 2.5723 0.6916
FKBP8 Layer 6 2.2969 0.6911
ATP6V0A1 Layer 5 2.5273 0.6911
PINK1 Layer 5 2.5059 0.6910
USP22 Layer 5 2.3896 0.6906
BEX2 Layer 5 2.3750 0.6906
SNU13 Layer 6 2.3750 0.6902
SULT4A1 Layer 5 2.5635 0.6899
CALY Layer 4 2.4941 0.6892
ARHGDIG Layer 6 2.5840 0.6891
ATP5PO Layer 6 2.3711 0.6886

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1361
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1361_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1361/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1361/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1361/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1361/report/PD/BN1361_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1361/report/PD/BN1361_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 03:54:01
  • Number of Processes: 10
  • Spending Time: 0h 3m